Imputation Report For Cohort: T1DGC

Per chromosome imputation report for cohort T1DGC.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 25.6.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 19825137 81.061
0.1 1220716 4.991
0.2 811180 3.317
0.3 617383 2.524
0.4 495654 2.027
0.5 405822 1.659
0.6 350865 1.435
0.7 291498 1.192
0.8 243858 0.997
0.9 194836 0.797
Total 24456949 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 1210935 4.951
0.4 1423015 5.818
0.5 1867916 7.638
0.6 2548371 10.420
0.7 3348915 13.693
0.8 3929440 16.067
0.9 10077196 41.204
1.0 51161 0.209
Total 24456949 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1486087 81.1978
0.1 89796 4.9063
0.2 57668 3.1509
0.3 45443 2.4829
0.4 37499 2.0489
0.5 30277 1.6543
0.6 27286 1.4909
0.7 22054 1.2050
0.8 18539 1.0129
0.9 15557 0.8500
Total 1830206

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 94103 5.1417
0.4 110587 6.0423
0.5 142147 7.7667
0.6 193896 10.5942
0.7 256776 14.0299
0.8 300367 16.4116
0.9 728962 39.8295
1.0 3368 0.1840
Total 1830206

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1662811 81.5407
0.1 100828 4.9444
0.2 65686 3.2211
0.3 49835 2.4438
0.4 38561 1.8909
0.5 32958 1.6162
0.6 28818 1.4132
0.7 23182 1.1368
0.8 20183 0.9897
0.9 16379 0.8032
Total 2039241

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 99413 4.8750
0.4 115324 5.6552
0.5 151650 7.4366
0.6 208854 10.2418
0.7 280634 13.7617
0.8 330728 16.2182
0.9 848139 41.5909
1.0 4499 0.2206
Total 2039241

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1390970 81.0401
0.1 88077 5.1315
0.2 55164 3.2139
0.3 43172 2.5153
0.4 35184 2.0499
0.5 29054 1.6927
0.6 24694 1.4387
0.7 20374 1.1870
0.8 16981 0.9893
0.9 12728 0.7416
Total 1716398

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 80628 4.6975
0.4 94206 5.4886
0.5 125548 7.3146
0.6 173484 10.1074
0.7 233821 13.6228
0.8 280927 16.3672
0.9 724290 42.1983
1.0 3494 0.2036
Total 1716398

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1343127 80.1888
0.1 82060 4.8992
0.2 60900 3.6359
0.3 45171 2.6968
0.4 33954 2.0272
0.5 27944 1.6683
0.6 24457 1.4602
0.7 21786 1.3007
0.8 20162 1.2037
0.9 15395 0.9191
Total 1674956

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 82084 4.9007
0.4 95995 5.7312
0.5 124988 7.4622
0.6 169946 10.1463
0.7 222383 13.2769
0.8 264227 15.7752
0.9 711580 42.4835
1.0 3753 0.2241
Total 1674956

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1264499 81.1756
0.1 76640 4.9200
0.2 53202 3.4153
0.3 39938 2.5639
0.4 31573 2.0269
0.5 24413 1.5672
0.6 22575 1.4492
0.7 18415 1.1822
0.8 14918 0.9577
0.9 11560 0.7421
Total 1557733

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 74315 4.7707
0.4 86716 5.5668
0.5 114117 7.3258
0.6 156386 10.0393
0.7 209398 13.4425
0.8 252928 16.2369
0.9 660762 42.4182
1.0 3111 0.1997
Total 1557733

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1227608 80.4389
0.1 80948 5.3041
0.2 52842 3.4625
0.3 40389 2.6465
0.4 32591 2.1355
0.5 25707 1.6844
0.6 22886 1.4996
0.7 16890 1.1067
0.8 15398 1.0090
0.9 10879 0.7128
Total 1526138

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 68286 4.4744
0.4 79661 5.2198
0.5 102653 6.7263
0.6 143681 9.4147
0.7 196849 12.8985
0.8 239492 15.6927
0.9 691159 45.2881
1.0 4357 0.2855
Total 1526138

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1118160 80.9665
0.1 69153 5.0074
0.2 47735 3.4565
0.3 35488 2.5697
0.4 28617 2.0722
0.5 23469 1.6994
0.6 19339 1.4003
0.7 16426 1.1894
0.8 12094 0.8757
0.9 10535 0.7628
Total 1381016

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 67796 4.9091
0.4 79488 5.7558
0.5 103720 7.5104
0.6 141391 10.2382
0.7 188494 13.6489
0.8 222759 16.1301
0.9 574319 41.5867
1.0 3049 0.2208
Total 1381016

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1123029 81.8572
0.1 64399 4.6940
0.2 44629 3.2530
0.3 32087 2.3388
0.4 27602 2.0119
0.5 21574 1.5725
0.6 19117 1.3934
0.7 15688 1.1435
0.8 13365 0.9742
0.9 10447 0.7615
Total 1371937

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 65922 4.8050
0.4 76176 5.5524
0.5 99454 7.2492
0.6 136807 9.9718
0.7 182164 13.2779
0.8 220679 16.0852
0.9 586441 42.7455
1.0 4294 0.3130
Total 1371937

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 841028 81.2864
0.1 53662 5.1865
0.2 33721 3.2592
0.3 25001 2.4164
0.4 20461 1.9776
0.5 15844 1.5313
0.6 14632 1.4142
0.7 11954 1.1554
0.8 9487 0.9169
0.9 8858 0.8561
Total 1034648

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 47681 4.6084
0.4 56010 5.4134
0.5 74228 7.1742
0.6 103263 9.9805
0.7 138681 13.4037
0.8 169944 16.4253
0.9 442441 42.7625
1.0 2400 0.2320
Total 1034648

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 962829 80.8750
0.1 60589 5.0893
0.2 39541 3.3213
0.3 28491 2.3932
0.4 24723 2.0767
0.5 20884 1.7542
0.6 17164 1.4417
0.7 13837 1.1623
0.8 12823 1.0771
0.9 9634 0.8092
Total 1190515

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 55118 4.6298
0.4 64439 5.4127
0.5 84966 7.1369
0.6 116820 9.8126
0.7 157222 13.2062
0.8 190246 15.9801
0.9 518897 43.5859
1.0 2807 0.2358
Total 1190515

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 954628 80.8470
0.1 58979 4.9949
0.2 36398 3.0825
0.3 30749 2.6041
0.4 24388 2.0654
0.5 20829 1.7640
0.6 17969 1.5218
0.7 14243 1.2062
0.8 12143 1.0284
0.9 10458 0.8857
Total 1180784

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 55086 4.6652
0.4 65116 5.5146
0.5 86155 7.2964
0.6 119488 10.1194
0.7 161734 13.6972
0.8 193790 16.4120
0.9 496577 42.0549
1.0 2838 0.2403
Total 1180784

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 911919 80.8957
0.1 56803 5.0390
0.2 35551 3.1537
0.3 30473 2.7032
0.4 22977 2.0383
0.5 19006 1.6860
0.6 16114 1.4295
0.7 12828 1.1380
0.8 12297 1.0909
0.9 9309 0.8258
Total 1127277

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 55116 4.8893
0.4 65199 5.7838
0.5 85388 7.5747
0.6 117973 10.4653
0.7 153564 13.6226
0.8 177338 15.7315
0.9 469916 41.6859
1.0 2783 0.2469
Total 1127277

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 676144 79.9792
0.1 43050 5.0923
0.2 27953 3.3065
0.3 22587 2.6718
0.4 17417 2.0602
0.5 15616 1.8472
0.6 12423 1.4695
0.7 11441 1.3533
0.8 9704 1.1479
0.9 9065 1.0723
Total 845400

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 38390 4.5410
0.4 45456 5.3769
0.5 60781 7.1896
0.6 85439 10.1063
0.7 115546 13.6676
0.8 136838 16.1862
0.9 361114 42.7152
1.0 1836 0.2172
Total 845400

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 622851 81.1604
0.1 39088 5.0934
0.2 26287 3.4253
0.3 18060 2.3533
0.4 15237 1.9855
0.5 11959 1.5583
0.6 9902 1.2903
0.7 9168 1.1946
0.8 8067 1.0512
0.9 6813 0.8878
Total 767432

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 36944 4.8140
0.4 43159 5.6238
0.5 57557 7.4999
0.6 79801 10.3984
0.7 105282 13.7187
0.8 121353 15.8129
0.9 321906 41.9459
1.0 1430 0.1863
Total 767432

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 550449 81.1002
0.1 33261 4.9005
0.2 22509 3.3164
0.3 16680 2.4575
0.4 14268 2.1022
0.5 11818 1.7412
0.6 8958 1.3198
0.7 7996 1.1781
0.8 6543 0.9640
0.9 6245 0.9201
Total 678727

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 34886 5.1399
0.4 41059 6.0494
0.5 54190 7.9841
0.6 73712 10.8603
0.7 93358 13.7549
0.8 107295 15.8083
0.9 273011 40.2240
1.0 1216 0.1792
Total 678727

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 607844 81.4816
0.1 38052 5.1009
0.2 22538 3.0212
0.3 19148 2.5668
0.4 14542 1.9494
0.5 11902 1.5955
0.6 10892 1.4601
0.7 9405 1.2607
0.8 6809 0.9127
0.9 4857 0.6511
Total 745989

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40768 5.4650
0.4 48274 6.4711
0.5 63216 8.4741
0.6 84446 11.3200
0.7 107629 14.4277
0.8 121432 16.2780
0.9 279448 37.4601
1.0 776 0.1040
Total 745989

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 527168 81.4811
0.1 29943 4.6281
0.2 23152 3.5785
0.3 15500 2.3957
0.4 13362 2.0653
0.5 11185 1.7288
0.6 9053 1.3993
0.7 7863 1.2153
0.8 5872 0.9076
0.9 3884 0.6003
Total 646982

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 37959 5.8671
0.4 44353 6.8554
0.5 59070 9.1301
0.6 77584 11.9917
0.7 95053 14.6918
0.8 103829 16.0482
0.9 228519 35.3208
1.0 615 0.0951
Total 646982

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 541540 80.6295
0.1 33697 5.0171
0.2 23566 3.5087
0.3 17736 2.6407
0.4 13923 2.0730
0.5 10821 1.6111
0.6 9472 1.4103
0.7 8070 1.2015
0.8 6634 0.9877
0.9 6181 0.9203
Total 671640

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33108 4.9294
0.4 39068 5.8168
0.5 51451 7.6605
0.6 71372 10.6265
0.7 93723 13.9544
0.8 108228 16.1140
0.9 273521 40.7243
1.0 1169 0.1741
Total 671640

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 409293 80.2817
0.1 29016 5.6914
0.2 18897 3.7066
0.3 13287 2.6062
0.4 9745 1.9115
0.5 8657 1.6980
0.6 7173 1.4070
0.7 6056 1.1879
0.8 4526 0.8878
0.9 3171 0.6220
Total 509821

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 31263 6.1322
0.4 37939 7.4416
0.5 49928 9.7932
0.6 63240 12.4044
0.7 75708 14.8499
0.8 80162 15.7236
0.9 171354 33.6106
1.0 227 0.0445
Total 509821

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 437263 81.2821
0.1 27104 5.0383
0.2 18005 3.3469
0.3 13491 2.5078
0.4 11238 2.0890
0.5 8914 1.6570
0.6 7749 1.4404
0.7 5978 1.1112
0.8 4504 0.8372
0.9 3711 0.6898
Total 537957

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 27732 5.1551
0.4 33011 6.1364
0.5 44529 8.2774
0.6 59398 11.0414
0.7 75055 13.9519
0.8 84795 15.7624
0.9 212628 39.5251
1.0 809 0.1504
Total 537957

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 254474 79.9232
0.1 15823 4.9696
0.2 10370 3.2569
0.3 9025 2.8345
0.4 7131 2.2396
0.5 5866 1.8423
0.6 4980 1.5641
0.7 4417 1.3873
0.8 4086 1.2833
0.9 2226 0.6991
Total 318398

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17086 5.3662
0.4 20014 6.2858
0.5 25958 8.1527
0.6 35475 11.1417
0.7 44720 14.0453
0.8 49212 15.4561
0.9 125521 39.4227
1.0 412 0.1294
Total 318398

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 258589 81.0535
0.1 15923 4.9910
0.2 11048 3.4629
0.3 7851 2.4609
0.4 6833 2.1418
0.5 5438 1.7045
0.6 4620 1.4481
0.7 4014 1.2582
0.8 2870 0.8996
0.9 1849 0.5796
Total 319035

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17981 5.6361
0.4 21811 6.8366
0.5 28002 8.7771
0.6 35979 11.2774
0.7 44253 13.8709
0.8 49022 15.3657
0.9 121496 38.0823
1.0 491 0.1539
Total 319035

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 652827 83.1925
0.1 33825 4.3105
0.2 23818 3.0352
0.3 17781 2.2659
0.4 13828 1.7622
0.5 11687 1.4893
0.6 10592 1.3498
0.7 9413 1.1995
0.8 5853 0.7459
0.9 5095 0.6493
Total 784719

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49270 6.2787
0.4 59954 7.6402
0.5 78220 9.9679
0.6 99936 12.7353
0.7 116868 14.8930
0.8 123849 15.7826
0.9 255195 32.5206
1.0 1427 0.1818
Total 784719

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering